Hello James, It appears that PeptideProphet invalidated all your spectrum matches hence the message: "read in 0 1+, 0 2+, 0 3+, 0 4+, 0 5+, 0 6+, 0 7+ spectra with min prob 0.05 no data - quitting". Please double check your raw data in a visualizer (e.g. Pep3D) to make sure that your LC worked ok. Then double check your search database and search parameters to make sure you are searching the right sequences and including all required modification. If that doesn't help you can try using a decoy database in your analysis to improve confidence in your analysis.
-David On Fri, Jun 26, 2009 at 2:10 PM, James Dowell<[email protected]> wrote: > > Hello, I've been searching SILAC data using X!Tandem within the TPP. > Everything works fine until I try to analyze my PeptideProphet hits > with ProteinProphet. I noticed that other people were having similar > problems with data from Bioworks and it was solved by moving the the > fasta database from the dbase folder to the database folder. However, > in my case this did not help. Also, I had to change a lot of settings > in the X!Tandem default file before I could get the database search to > work. Is it possible that my params file would have something to do > with this. > > Thanks for your help. > > I get the following error message: > > # Commands for session JDZWDT2EB on Fri Jun 26 15:38:54 2009 > # BEGIN COMMAND BLOCK > ###### BEGIN Command Execution ###### > [Fri Jun 26 15:38:54 2009] EXECUTING: ProteinProphet c:/Inetpub/ > wwwroot/ISB/data/JD032609_SILAC1_F6.tandem.pep.xml c:/Inetpub/wwwroot/ > ISB/data/interact.prot.xml EXCLUDE_ZEROS > OUTPUT: > ProteinProphet (C++) by Insilicos LLC and LabKey Software, after the > original Perl by A. Keller (TPP v4.2 JETSTREAM rev 1, Build > 200904071723 (MinGW)) > (xml input) (report Protein Length) (using degen pep info) (exclude > zero prob entries) > . . . reading in c:/Inetpub/wwwroot/ISB/data/ > JD032609_SILAC1_F6.tandem.pep.xml. . . > . . . read in 0 1+, 0 2+, 0 3+, 0 4+, 0 5+, 0 6+, 0 7+ spectra with > min prob 0.05 > no data - quittingEND OUTPUT > RETURN CODE:256 > ###### End Command Execution ###### > # All finished at Fri Jun 26 15:38:54 2009 > # END COMMAND BLOCK > > > > > --~--~---------~--~----~------------~-------~--~----~ You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To post to this group, send email to [email protected] To unsubscribe from this group, send email to [email protected] For more options, visit this group at http://groups.google.com/group/spctools-discuss?hl=en -~----------~----~----~----~------~----~------~--~---
